You know what happens to a tree during a drought when it goes through periods of not being watered? It's roots grow deeper extending in search for water. It's an interesting growth process. Just like a man digging a well continues to dig deeper until hitting water, so does a tree. On the surface the tree may appear to be stunted, bearing less or no fruit, and hardly gaining any mass, but that is because it's attention is drawn below the ground where it's growing more than ever before.
This is a normal growth process. If the trees had all the nutrients they needed on the surface, it's roots would need not dig and remain shallow. The first decent windstorm would send it toppling. By extending it's roots the tree becomes more firmly planted. The tree's unseen growth will further it's seen growth.
This process can entail any of the previous mentioned origins of doubt. They are all part of the growth process. What's important to understand is, God can be using this process to further your growth, regardless of the avenue He chooses. Peter in fear denied being with Jesus (Luke 22:54-62), and later it was Peter who publicly held accountable those very same people who crucified Christ (Acts 2:23).
I have mentioned Hebrews 12:2 that God is the author of our faith as stated, but notice also He is the perfecter of our faith. Let me show you it in the Amplified version:
Looking away [from all that will distract] to Jesus, Who is the Leader and the Source of our faith [giving the first incentive for our belief] and is also its Finisher [bringing it to maturity and perfection]. He, for the joy [of obtaining the prize] that was set before Him, endured the cross, despising and ignoring the shame, and is now seated at the right hand of the throne of God. - Hebrews 12:2 (Amplified)
This growth process takes time. While our salvation is instant the moment we said Yes to Jesus, our maturity is being worked on.
For I am confident of this very thing, that He who began a good work in you will perfect it until the day of Christ Jesus. - Phillipians 1:6
God can see your true needs better than anyone including yourself. And He can work according to His will for your good as He sees fit (Rom. 8:28). Do not let me lessen any solution already discussed, as 2 Corinthians 1:4 teaches, comfort we're given from another is really comfort supplied by God through that person. I just want to point out that God is God and is not limited or restricted in how He works in your life in any way.
One verse that a fellow child in Christ shared with me that resounded in every area of my struggle was this. "Be still, and know that I am God..." - Psalm 46:10 (NKJV). But take note that whether you are still or not, whether you strive or rest, He is still God and there is nothing you can do to change that. The very same God who is for you (Rom. 8:31), and who desires to give you the kingdom (Luke 12:32).
"Every branch in Me that does not bear fruit, He takes away; and every branch that bears fruit, He prunes it so that it may bear more fruit. - John 15:2
Undergoing the actual process of being pruned is not pleasant at all. Like a tree, your dead parts are being cut away from your parts that are alive (cf Col. 2:13). However, the end result of this pruning is far too valuable to the Pruner to not follow through with it.
God is our Pruner, and it is God who causes the growth (1 Cor. 3:7). Therefore there is no specific solution to this type of doubt. While all the earlier solutions can be applied to each's specific type of doubt; to attempt to narrow this one down is to attempt to put limits on God. One promise we can count on of our Pruner however:
And we know that God causes all things to work together for good to those who love God, to those who are called according to His purpose. - Rom. 8:28
This doesn't mean that all things will be pleasant, I think Paul would spit his soda out if someone were to say that. (cf 2 Cor. 12:7-8). But it does mean that God can use ALL things to our good according to His purpose.